As a student in Claremont, Griffin was initially interested in Eastern religions, particularly Vedanta. However, he started to become a process theologian while attending John B. Cobb’s seminar on Whitehead’s philosophy. According to Griffin, process theology, as presented by Cobb, “provided a way between the old supernaturalism, according to which God miraculously interrupted the normal causal processes now and then, and a view according to which God is something like a cosmic hydraulic jack, exerting the same pressure always and everywhere (which described rather aptly the position to which I had come)" (Primordial Truth and Postmodern Theology). Griffin applied Whitehead’s thought to the traditional theological subjects of christology and theodicy and argued that process theology also provided a sound basis for addressing contemporary social and ecological issues.[5]

After teaching theology and Eastern religions at the University of Dayton, Griffin came to appreciate the distinctively postmodern aspects of Whitehead's thought. In particular, Griffin found Whitehead's nonsensationist epistemology and panexperientialist ontology immensely helpful in addressing the major problems of modern philosophy, including the problems of mind-body interaction, the interaction between free and determined things, the emergence of experience from nonexperiencing matter, and the emergence of time in the evolutionary process. In 1973, Griffin returned to Claremont to establish, with Cobb, the Center for Process Studies at the Claremont School of Theology.[6]

While on research leave in 1980–81 at Cambridge University and Berkeley, the contrast between modernity and postmodernity became central to his work. Many of Griffin’s writings are devoted to developing postmodern proposals for overcoming the conflicts between religion and modern science. Griffin came to believe that much of the tension between religion and science was not only the result of reactionary supernaturalism but also the mechanistic worldview associated with the rise of modern science in the seventeenth century. In 1983, Griffin started the Center for a Postmodern World in Santa Barbara and became editor of the SUNY Series in Constructive Postmodern Philosophy between 1987 and 2004.[7]

"Until the spring of 2003, I had not looked at any of the evidence. I was vaguely aware there were people, at least on the internet, who were offering evidence against the official account of 9/11... I knew the US government had 'fabricated' evidence to go to war several times before. Nevertheless... I did not take this possibility seriously... I was so confident that they must be wrong." [8]

Part One of the book looks at the events of 9/11, discussing each flight in turn and also the behaviour of President George W. Bush and his Secret Service protection. Part Two examines 9/11 in a wider context, in the form of four "disturbing questions." David Ray Griffin discussed this book and the claims within it in an interview with Nick Welsh, reported under the headline Thinking Unthinkable Thoughts: Theologian Charges White House Complicity in 9/11 Attack.[10]

Critics of Griffin's thesis, such as Chip Berlet, have said that many of the claims in the book are refutable.[11] Griffin has rejected these criticisms[12] and debated Berlet.[13]

Griffin's second book on the subject was a direct critique of the 9/11 Commission Report, called The 9/11 Commission Report: Omissions And Distortions (2005).[14] Griffin's article The 9/11 Commission Report: A 571-page Lie summarizes this book, presenting 115 instances of either omissions or distortions of evidence he claims are in the report, stating that "the entire Report is constructed in support of one big lie: that the official story about 9/11 is true."[15]

In his next book, Christian Faith and the Truth Behind 9/11: A Call to Reflection and Action (2006), he summarizes some of what he believes is evidence for government complicity and reflects on its implications for Christians. The Presbyterian Publishing Corporation, publishers of the book, noted that Griffin is a distinguished theologian and praised the book’s religious content, but said, "The board believes the conspiracy theory is spurious and based on questionable research."[16][17]

In 2006, Griffin, along with Peter Dale Scott, edited 9/11 and the American Empire: Intellectuals Speak Out, a collection of essays including Steven Jones' paper Why Indeed Did The World Trade Center Towers Collapse?.[18]Debunking 9/11 Debunking (2007) looks at the way mainstream media such as Popular Mechanics have sought to debunk the alternative 9/11 theories and the tactics he claims they employ to persuade the reader that they have done so.[19] In 9/11 Contradictions: An Open Letter to Congress and the Press (2008), he presents chapters on 25 alleged contradictions involving elements of the "accepted story" of 9/11 and calls for Congress and the press to investigate and resolve them.[20]

David Ray Griffin has delivered several lectures that are popular within the 9/11 Truth Movement and has given interviews on alternative media shows such as The Alex Jones Show.[21] A lecture entitled 9/11 and American Empire: How should religious people respond?, delivered on April 18, 2005, at the University of Wisconsin–Madison, was aired by C-SPAN.[22] At the end of one of his lectures entitled 9/11: The Myth and the Reality Griffin was asked why a theologian would take such an interest in 9/11, to which he replied: "If 9/11 is not a religious issue, then I don't know what is."[23]

In a review published in the magazine The Nation, former Central Intelligence Agency agent Robert Baer dismissed the gist of Griffin's writings as one in a long line of conspiracy theories about national tragedies but stated that the Bush administration had created a climate of secrecy and mistrust that helped generate such explanations.[24] In the review, Baer said:

"As more facts emerge about September 11, many of Griffin's questions should be answered, but his suspicions will never be put to rest as long as the Bush Administration refuses to explain why it dragged this country into the most senseless war in its history. Until then, otherwise reasonable Americans will believe the Bush Administration benefited from 9/11, and there will always be a question about what really happened on that day."

Religion and Scientific Naturalism: Overcoming the Conflicts (SUNY Series in Constructive Postmodern Thought),State University of New York Press, 2000, ISBN 0-7914-4563-1

Process Theology and the Christian Good News: A Response to Classical Free Will Theism in 'Searching for an Adequate God: A Dialogue between Process and Free Will Theists', Cobb and Pinnock (editors), Wm. B. Eerdmans Publishing, 2000, ISBN 0-8028-4739-0

Two Great Truths: A New Synthesis of Scientific Naturalism and Christian Faith, Westminster John Knox Press, 2004, ISBN 0-664-22773-2